Hi, Maya-
There are a couple ways to get this info.
To see the labeltable in an ROI file that has them (and those *REN* files have 'em), you can run:
3dinfo -labeltable aparc.a2009s+aseg_REN_gmrois.nii.gz
In your AFNI binaries directory, you can also see the files used to create those labels, which are called:
afni_fs_aparc+aseg_2000.txt
afni_fs_aparc+aseg_2009.txt
The numbers match the respective output names.
In tcsh you could do:
set aa = `which afni`
cat ${aa:h}/afni_fs_aparc+aseg_2009.txt
... for example.
I think the cerebellum values in the full atlas are:
# FS_NUM STRING_LABEL TISS__TYPE REN_VAL COLOR_LUT
7 Left-Cerebellum-White-Matter tiss__wmat 5 220 248 164 0
8 Left-Cerebellum-Cortex tiss__gm 6 230 148 34 0
46 Right-Cerebellum-White-Matter tiss__wmat 25 220 248 164 0
47 Right-Cerebellum-Cortex tiss__gm 26 230 148 34 0
Only the GM ones will be in the *REN_gmrois* one, so you just need to excise ROI #6 and 26. You could do this with 3dcalc in different ways; one is to use the full dataset and subtract away the ROIs you don't want, which seems useful here since it is a short list:
3dcalc \
-a aparc.a2009s+aseg_REN_gmrois.nii.gz \
-b aparc.a2009s+aseg_REN_gmrois.nii.gz"<Left-Cerebellum-Cortex,Right-Cerebellum-Cortex>" \
-expr 'a-b' \
-prefix aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz
If you are only excising some integer values and not renumbering otherwise, you can reattach the original labeltable. To reattach a labeltable and integer-valued colormap (for looking at it in the AFNI GUI) afterward, you can:
3drefit -copytables aparc.a2009s+aseg_REN_gmrois.nii.gz aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz
3drefit -cmap INT_CMAP aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz
These are often convenient to do.
--pt
Edited 1 time(s). Last edit at 11/25/2022 10:12AM by ptaylor.
